Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 87 of 208
Found at i:25635380 original size:126 final size:131
Alignment explanation
Indices: 25635226--25635514 Score: 410
Period size: 126 Copynumber: 2.2 Consensus size: 131
25635216 ATGACCCTAG
*
25635226 CCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTAAGCAGCAG
1 CCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTAAGCAGCAA
* * *
25635291 TGGAATAGATT-AA-A-G-AA-TCCTATCTCCCTAGACAGCAGTGGAATAGGTTAAAGATTGTGA
66 TGGAATAGATTGAAGATGTAAGTCCTATATCCCTAGACAGCAGTGGAATAAGTTAAAGATCGTGA
25635351 A
131 A
* *
25635352 TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTAGGCAGCAA
1 CCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTAAGCAGCAA
* * * **
25635417 TGGAATAGATTGAAGATTGTAAGTCCTATATCCCTGGTCAGTAGTGGAATAAGTTGTAGATCGTG
66 TGGAATAGATTGAAGA-TGTAAGTCCTATATCCCTAGACAGCAGTGGAATAAGTTAAAGATCGTG
25635482 AA
130 AA
*
25635484 CCCTATCTCCCTGAG-CAGCAGTGGAGTAGGT
1 CCCTATCTCCCTG-GTCAGCAGTGGAATAGGT
25635515 GGAAAATAGA
Statistics
Matches: 143, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
126 73 0.51
127 2 0.01
128 1 0.01
130 1 0.01
131 2 0.01
132 63 0.44
133 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (131 bp):
CCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTAAGCAGCAA
TGGAATAGATTGAAGATGTAAGTCCTATATCCCTAGACAGCAGTGGAATAAGTTAAAGATCGTGA
A
Found at i:25635914 original size:44 final size:44
Alignment explanation
Indices: 25635821--25635924 Score: 120
Period size: 44 Copynumber: 2.4 Consensus size: 44
25635811 ATGACAAATT
* * *
25635821 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATC
1 TTATCTCCCTGAAGTTACAGTGAAGCAGATTAAAACCGATAATC
* * * *
25635865 CTATCTCCCTGAAGTTACAGTGAAGCGGATTAAAACC-TTGGATC
1 TTATCTCCCTGAAGTTACAGTGAAGCAGATTAAAACCGAT-AATC
*
25635909 TTATCTCTCTGAAGTT
1 TTATCTCCCTGAAGTT
25635925 GCAGAGAGCA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 1 0.02
44 49 0.98
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTACAGTGAAGCAGATTAAAACCGATAATC
Found at i:25636397 original size:17 final size:17
Alignment explanation
Indices: 25636345--25636397 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 17
25636335 TATGGAAACA
* *
25636345 TAATCTTCGAGGATATG
1 TAATCTTAGAAGATATG
*
25636362 CAATCTTAGATATGATATG
1 TAATCTTAGA-A-GATATG
25636381 TAATCTTAGAAGATATG
1 TAATCTTAGAAGATATG
25636398 ATTTTGTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 14 0.47
18 1 0.03
19 15 0.50
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (17 bp):
TAATCTTAGAAGATATG
Found at i:25636397 original size:22 final size:23
Alignment explanation
Indices: 25636369--25636413 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
25636359 ATGCAATCTT
25636369 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
25636391 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
25636414 GATTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:25636423 original size:22 final size:23
Alignment explanation
Indices: 25636379--25636423 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
25636369 AGATATGATA
*
25636379 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
25636402 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
25636424 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:25636610 original size:19 final size:21
Alignment explanation
Indices: 25636586--25636624 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
25636576 GCTTATTGTT
*
25636586 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
25636605 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
25636625 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:25636853 original size:3 final size:3
Alignment explanation
Indices: 25636845--25636885 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
25636835 ATTAATTTTG
25636845 TTA TTA TTA TTA TTA TTA TTA -TA TATA TATA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA TTA TTA TTA T
25636886 ACCTACATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 27 0.75
4 7 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:25636895 original size:19 final size:19
Alignment explanation
Indices: 25636855--25636895 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
25636845 TTATTATTAT
* *
25636855 TATTATTATTATATATATA
1 TATTATTATTATACATACA
*
25636874 TATTATTATTATACCTACA
1 TATTATTATTATACATACA
25636893 TAT
1 TAT
25636896 ATGTGCGCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTATTATTATACATACA
Found at i:25636895 original size:25 final size:25
Alignment explanation
Indices: 25636849--25636897 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
25636839 ATTTTGTTAT
* *
25636849 TATTATTATTATTATTATATATATA
1 TATTATTATTATTACTACATATATA
25636874 TATTATTATTA-TACCTACATATAT
1 TATTATTATTATTA-CTACATATAT
25636898 GTGCGCATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (25 bp):
TATTATTATTATTACTACATATATA
Found at i:25637260 original size:2 final size:2
Alignment explanation
Indices: 25637253--25637302 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
25637243 CATTATGTAT
25637253 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25637295 TA TA TA TA
1 TA TA TA TA
25637303 AGTTTTATAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25641694 original size:18 final size:18
Alignment explanation
Indices: 25641658--25641696 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
25641648 TTATTATTTT
*
25641658 TAAAATTTACTATTGAAA
1 TAAAATTTAATATTGAAA
25641676 TAAAATTTAAATATT-AAA
1 TAAAATTT-AATATTGAAA
25641694 TAA
1 TAA
25641697 TTTATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAAATTTAATATTGAAA
Found at i:25641814 original size:13 final size:14
Alignment explanation
Indices: 25641791--25641823 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
25641781 AATATTAAAA
25641791 ATATATAATATTTT
1 ATATATAATATTTT
25641805 ATAT-TAATATTTT
1 ATATATAATATTTT
*
25641818 AAATAT
1 ATATAT
25641824 TTTTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATATAATATTTT
Found at i:25644504 original size:27 final size:27
Alignment explanation
Indices: 25644466--25644562 Score: 155
Period size: 27 Copynumber: 3.7 Consensus size: 27
25644456 AAAGTTAAAA
25644466 AGTATATATTATATAATATTAAAACTT
1 AGTATATATTATATAATATTAAAACTT
*
25644493 AGTATAAATTATAT--TA-TAAAACTT
1 AGTATATATTATATAATATTAAAACTT
25644517 AGTATATATTATATAATATTAAAACTT
1 AGTATATATTATATAATATTAAAACTT
*
25644544 AGTATATATTATATTATAT
1 AGTATATATTATATAATAT
25644563 ATTATATTAT
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
24 21 0.33
25 2 0.03
26 2 0.03
27 39 0.61
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.45
Consensus pattern (27 bp):
AGTATATATTATATAATATTAAAACTT
Found at i:25644563 original size:12 final size:12
Alignment explanation
Indices: 25644546--25644574 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
25644536 TAAAACTTAG
25644546 TATATATTATAT
1 TATATATTATAT
25644558 TATATATTATAT
1 TATATATTATAT
25644570 TATAT
1 TATAT
25644575 TAATAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATATATTATAT
Found at i:25645662 original size:40 final size:40
Alignment explanation
Indices: 25645541--25645680 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
25645531 GACTTCGAGT
* * * *
25645541 CGATGAGACATTGGGTGTCAATTTATTACTTTAGATTAATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTCAGATT-ATC
* * * * *
25645582 CGATGAGGCACTGGGTG-CCAA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCAGATTATC
* *
25645619 CGATGAGACACTGGGTGTCAAATTATTACTTCAAAATATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCAGATTATC
* * *
25645659 CGATGAGGCATTGGGTGCCAAA
1 CGATGAGACACTGGGTGTCAAA
25645681 CTGGTGTATT
Statistics
Matches: 77, Mismatches: 19, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
37 17 0.22
38 12 0.16
39 2 0.03
40 31 0.40
41 15 0.19
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.31
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCAGATTATC
Found at i:25647908 original size:29 final size:31
Alignment explanation
Indices: 25647876--25647936 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 31
25647866 AAACCTTTTT
*
25647876 ACTTTCCCCCCAATA-TTTTAC-TCCCTCCC
1 ACTTTCCCCCCAAAACTTTTACTTCCCTCCC
*
25647905 ACTTTCCCCCCAAAACTTTTACTTTCCTCCC
1 ACTTTCCCCCCAAAACTTTTACTTCCCTCCC
25647936 A
1 A
25647937 TCCCAACCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 14 0.50
30 6 0.21
31 8 0.29
ACGTcount: A:0.20, C:0.46, G:0.00, T:0.34
Consensus pattern (31 bp):
ACTTTCCCCCCAAAACTTTTACTTCCCTCCC
Found at i:25656284 original size:26 final size:26
Alignment explanation
Indices: 25656254--25656312 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
25656244 AAACTTTTCT
*
25656254 AAAAGAAGCTTAAGAGAAATTCTTAA
1 AAAAGAAGCTCAAGAGAAATTCTTAA
25656280 AAAAGAAGCTCAAGAGAAATTCTTAA
1 AAAAGAAGCTCAAGAGAAATTCTTAA
25656306 AAAAGAA
1 AAAAGAA
25656313 AACTCAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.58, C:0.08, G:0.15, T:0.19
Consensus pattern (26 bp):
AAAAGAAGCTCAAGAGAAATTCTTAA
Found at i:25656333 original size:27 final size:26
Alignment explanation
Indices: 25656254--25656325 Score: 99
Period size: 26 Copynumber: 2.7 Consensus size: 26
25656244 AAACTTTTCT
* *
25656254 AAAAGAAGCTTAAGAGAAATTCTTAA
1 AAAAGAAACTCAAGAGAAATTCTTAA
*
25656280 AAAAGAAGCTCAAGAGAAATTCTTAA
1 AAAAGAAACTCAAGAGAAATTCTTAA
25656306 AAAAGAAAACTCAAAGAGAA
1 AAAAG-AAACTC-AAGAGAA
25656326 TTTATAAACT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
26 30 0.71
27 5 0.12
28 7 0.17
ACGTcount: A:0.58, C:0.10, G:0.15, T:0.17
Consensus pattern (26 bp):
AAAAGAAACTCAAGAGAAATTCTTAA
Found at i:25672939 original size:13 final size:12
Alignment explanation
Indices: 25672921--25672981 Score: 68
Period size: 13 Copynumber: 4.8 Consensus size: 12
25672911 ATTTTCCTAC
25672921 TTTATTATTATTA
1 TTTATTATT-TTA
*
25672934 TTTATTTTTTTA
1 TTTATTATTTTA
25672946 TTCTATTATTTTA
1 TT-TATTATTTTA
*
25672959 TTTCTTTATTTTA
1 TTT-ATTATTTTA
25672972 TTTTATTATT
1 -TTTATTATT
25672982 CGGTTTATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
12 6 0.15
13 32 0.78
14 3 0.07
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:25672947 original size:21 final size:21
Alignment explanation
Indices: 25672920--25672981 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
25672910 CATTTTCCTA
25672920 CTTTATTATTATTA-TTTATTT
1 CTTTATT-TTATTATTTTATTT
* *
25672941 TTTTATTCTATTATTTTATTT
1 CTTTATTTTATTATTTTATTT
25672962 CTTTATTTTATT-TTATTATT
1 CTTTATTTTATTATT-TTATT
25672982 CGGTTTATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 7 0.20
21 28 0.80
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (21 bp):
CTTTATTTTATTATTTTATTT
Found at i:25672952 original size:26 final size:26
Alignment explanation
Indices: 25672923--25672981 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
25672913 TTTCCTACTT
25672923 TATTATTATTATTTATTT-TTTTATTC
1 TATTATT-TTATTTATTTATTTTATTC
* *
25672949 TATTATTTTATTTCTTTATTTTATTT
1 TATTATTTTATTTATTTATTTTATTC
25672975 TATTATT
1 TATTATT
25672982 CGGTTTATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 9 0.30
26 21 0.70
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (26 bp):
TATTATTTTATTTATTTATTTTATTC
Found at i:25673309 original size:33 final size:34
Alignment explanation
Indices: 25673235--25673310 Score: 82
Period size: 36 Copynumber: 2.2 Consensus size: 34
25673225 TTTTAGTTTA
* *
25673235 TTATTATAGTTACTACTATTATTCGTCCTTATTT
1 TTATTATAGTTACTACTATGATTCGTCCTTATGT
* * *
25673269 TACTATTATGGTTATTATTATGATTCGTCCTTA-GT
1 T--TATTATAGTTACTACTATGATTCGTCCTTATGT
25673304 TTATTAT
1 TTATTAT
25673311 TTTGAATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
33 6 0.17
34 1 0.03
35 2 0.06
36 26 0.74
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.55
Consensus pattern (34 bp):
TTATTATAGTTACTACTATGATTCGTCCTTATGT
Found at i:25674932 original size:6 final size:6
Alignment explanation
Indices: 25674923--25674956 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
25674913 TTTGTTTTCT
25674923 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
25674957 TATGTTTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:25674981 original size:6 final size:6
Alignment explanation
Indices: 25674917--25675008 Score: 58
Period size: 6 Copynumber: 14.5 Consensus size: 6
25674907 ATTTTATTTG
* * * * * *
25674917 TTTTCT TTTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTTAT GTTTAT
1 TTTTAT TTTT-AT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* * *
25674966 GTTTATT TTTTAT TTTTAGTT GTTTTGT TTTTTT TTTTAT TTT
1 TTTTA-T TTTTAT TTTTA--T -TTTTAT TTTTAT TTTTAT TTT
25675009 CTTATAGTTC
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
6 58 0.79
7 10 0.14
8 1 0.01
9 4 0.05
ACGTcount: A:0.17, C:0.01, G:0.05, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:25674994 original size:26 final size:26
Alignment explanation
Indices: 25674915--25675008 Score: 79
Period size: 25 Copynumber: 3.7 Consensus size: 26
25674905 TGATTTTATT
* * *
25674915 TGTTTTCTTTTTAATTTTAAT-TTTA
1 TGTTTTATTTTTTATTTTTATGTTTA
* * *
25674940 -ATTTTAATTTTAATTTTTATGTTTA
1 TGTTTTATTTTTTATTTTTATGTTTA
25674965 TG-TTTATTTTTTATTTTTAGTTGTTT-
1 TGTTTTATTTTTTATTTTTA--TGTTTA
*
25674991 TGTTTTTTTTTTTATTTT
1 TGTTTTATTTTTTATTTT
25675009 CTTATAGTTC
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
24 16 0.29
25 19 0.34
26 2 0.04
27 19 0.34
ACGTcount: A:0.17, C:0.01, G:0.06, T:0.76
Consensus pattern (26 bp):
TGTTTTATTTTTTATTTTTATGTTTA
Found at i:25675001 original size:27 final size:25
Alignment explanation
Indices: 25674942--25675008 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 25
25674932 TAATTTTAAT
* *
25674942 TTTAATTTTAATTTTTATGTTTATG
1 TTTATTTTTTATTTTTATGTTTATG
25674967 TTTATTTTTTATTTTTAGTTGTTT-TG
1 TTTATTTTTTATTTTTA--TGTTTATG
*
25674993 TTTTTTTTTTTATTTT
1 -TTTATTTTTTATTTT
25675009 CTTATAGTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 15 0.42
26 2 0.06
27 19 0.53
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (25 bp):
TTTATTTTTTATTTTTATGTTTATG
Found at i:25677524 original size:36 final size:36
Alignment explanation
Indices: 25677434--25677541 Score: 191
Period size: 36 Copynumber: 3.0 Consensus size: 36
25677424 AATTAGAAAG
25677434 AGATTTCAATTAATCAACTTAGAGTCAGTTGTTCTT
1 AGATTTCAATTAATCAACTTAGAGTCAGTTGTTCTT
* *
25677470 AGATTTC-ATTAATCAACTTAAAGTGAGTTGTTCTT
1 AGATTTCAATTAATCAACTTAGAGTCAGTTGTTCTT
25677505 AGATTTCAATTAATCAACTTAGAGTCAGTTGTTCTT
1 AGATTTCAATTAATCAACTTAGAGTCAGTTGTTCTT
25677541 A
1 A
25677542 CTCTCGAAAG
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
35 33 0.49
36 34 0.51
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (36 bp):
AGATTTCAATTAATCAACTTAGAGTCAGTTGTTCTT
Found at i:25677984 original size:9 final size:9
Alignment explanation
Indices: 25677970--25678005 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
25677960 AAATTATAAG
25677970 TTTTTTTTC
1 TTTTTTTTC
25677979 TTTTTTTTC
1 TTTTTTTTC
25677988 TTTTTTTTC
1 TTTTTTTTC
25677997 TTTTCTTTT
1 TTTT-TTTT
25678006 ACTTAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 22 0.85
10 4 0.15
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:25680595 original size:42 final size:42
Alignment explanation
Indices: 25680536--25680620 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
25680526 TGATTACAAG
25680536 TTAGTGCATTTAAACATAGCACTTTTGGAATCAACTTCATGA
1 TTAGTGCATTTAAACATAGCACTTTTGGAATCAACTTCATGA
25680578 TTAGTGCATTTAAACATAGCACTTTTGGAATCAACTTCATGA
1 TTAGTGCATTTAAACATAGCACTTTTGGAATCAACTTCATGA
25680620 T
1 T
25680621 AAACCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (42 bp):
TTAGTGCATTTAAACATAGCACTTTTGGAATCAACTTCATGA
Found at i:25688790 original size:46 final size:46
Alignment explanation
Indices: 25688718--25688838 Score: 136
Period size: 46 Copynumber: 2.6 Consensus size: 46
25688708 TTTATCATGT
* * * * *
25688718 TTGAAGTGTTAAAGTGTTGCATATTGAAGTATTTATATGCTGTGAA
1 TTGAAGTGTTAAAGTGCTGCAAATTGAAGTATTTAAATGCTATAAA
* *
25688764 TTGAAGTGTTAAAGTGCTGCAAATTGAAGTGTTTAAATGTTATAAA
1 TTGAAGTGTTAAAGTGCTGCAAATTGAAGTATTTAAATGCTATAAA
* *
25688810 TGGAAGTGTTTTAAA-TACTGCAAATTGAA
1 TTGAAGTG--TTAAAGTGCTGCAAATTGAA
25688839 TTGTTTAGTT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
46 46 0.72
47 13 0.20
48 5 0.08
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (46 bp):
TTGAAGTGTTAAAGTGCTGCAAATTGAAGTATTTAAATGCTATAAA
Found at i:25688810 original size:23 final size:23
Alignment explanation
Indices: 25688718--25688910 Score: 115
Period size: 23 Copynumber: 8.4 Consensus size: 23
25688708 TTTATCATGT
* *
25688718 TTGAAGTG-TTAAAGTGTTGCATA
1 TTGAAGTGTTTAAA-TGCTGCAAA
* * **
25688741 TTGAAGTATTTATATGCTGTGAA
1 TTGAAGTGTTTAAATGCTGCAAA
25688764 TTGAAGTG-TTAAAGTGCTGCAAA
1 TTGAAGTGTTTAAA-TGCTGCAAA
* **
25688787 TTGAAGTGTTTAAATGTTATAAA
1 TTGAAGTGTTTAAATGCTGCAAA
* *
25688810 TGGAAGTGTTTTAAATACTGCAAA
1 TTGAAGTG-TTTAAATGCTGCAAA
* ** *
25688834 TTGAATTGTTTAGTTGCTGAAAA
1 TTGAAGTGTTTAAATGCTGCAAA
* * *
25688857 TTG-AGATGTTTTATTGCTG-TAA
1 TTGAAG-TGTTTAAATGCTGCAAA
* * * * *
25688879 CTGAGGTGTATAAATGTTGTAAA
1 TTGAAGTGTTTAAATGCTGCAAA
25688902 TTGAAGTGT
1 TTGAAGTGT
25688911 CTATTGCTGA
Statistics
Matches: 126, Mismatches: 37, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
22 18 0.14
23 82 0.65
24 26 0.21
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.40
Consensus pattern (23 bp):
TTGAAGTGTTTAAATGCTGCAAA
Found at i:25688834 original size:24 final size:24
Alignment explanation
Indices: 25688762--25688844 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
25688752 ATATGCTGTG
*
25688762 AATTGAAGTG--TTAAAGTGCTGCA
1 AATTGAAGTGTTTTAAA-TACTGCA
** **
25688785 AATTGAAGTG-TTTAAATGTTATA
1 AATTGAAGTGTTTTAAATACTGCA
*
25688808 AATGGAAGTGTTTTAAATACTGCA
1 AATTGAAGTGTTTTAAATACTGCA
*
25688832 AATTGAATTGTTT
1 AATTGAAGTGTTT
25688845 AGTTGCTGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 23 0.48
24 25 0.52
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (24 bp):
AATTGAAGTGTTTTAAATACTGCA
Found at i:25689293 original size:38 final size:36
Alignment explanation
Indices: 25689225--25689301 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 36
25689215 TAGAGTATTA
*
25689225 TATATTATGATTTTAATAAATTCATATAATAATAAT
1 TATATTAAGATTTTAATAAATTCATATAATAATAAT
*
25689261 TATATTAAGAATTTTATTAAATT-ATATTTAATAATAAT
1 TATATTAAG-ATTTTAATAAATTCATA--TAATAATAAT
25689299 TAT
1 TAT
25689302 GCTAAAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
36 11 0.31
37 12 0.33
38 13 0.36
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (36 bp):
TATATTAAGATTTTAATAAATTCATATAATAATAAT
Found at i:25695317 original size:49 final size:49
Alignment explanation
Indices: 25695260--25695363 Score: 154
Period size: 49 Copynumber: 2.1 Consensus size: 49
25695250 TCATGTGTTA
* * ** * *
25695260 TAATTTTATACAGTGTTGAGTTTTTTATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
25695309 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
25695358 TAATTT
1 TAATTT
25695364 GTTTTTTTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.52
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:25696171 original size:44 final size:46
Alignment explanation
Indices: 25696121--25696210 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
25696111 CCTCTATTCT
*
25696121 ATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCCATTAC
1 ATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTAC
*
25696165 ATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCTATTAC
1 ATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTAC
25696211 GCCTCTATTC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 18 0.43
45 4 0.10
46 20 0.48
ACGTcount: A:0.39, C:0.29, G:0.04, T:0.28
Consensus pattern (46 bp):
ATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTAC
Found at i:25696209 original size:16 final size:16
Alignment explanation
Indices: 25696190--25696242 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
25696180 AGAATTACCT
*
25696190 ATTACGCCTCTATTCT
1 ATTACGCCTCTATTCC
25696206 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
25696222 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
25696238 ATTAC
1 ATTAC
25696243 AGCGAACCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:25696210 original size:46 final size:45
Alignment explanation
Indices: 25696113--25696210 Score: 146
Period size: 44 Copynumber: 2.2 Consensus size: 45
25696103 CTATTACACC
*
25696113 TCTATT-CTATTCAACCAAACACAAGAATACCATTACGCCTCTAT
1 TCTATTACTATTCAACCAAACAAAAGAATACCATTACGCCTCTAT
*
25696157 TCCATTAC-ATTCAACCAAACAAAAGAATTACCTATTACGCCTCTAT
1 TCTATTACTATTCAACCAAACAAAAGAA-TACC-ATTACGCCTCTAT
25696203 TCTATTAC
1 TCTATTAC
25696211 GCCTCTATTC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
44 23 0.48
45 5 0.10
46 20 0.42
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.31
Consensus pattern (45 bp):
TCTATTACTATTCAACCAAACAAAAGAATACCATTACGCCTCTAT
Found at i:25696330 original size:38 final size:38
Alignment explanation
Indices: 25696230--25696319 Score: 180
Period size: 38 Copynumber: 2.4 Consensus size: 38
25696220 CCATTACGCC
25696230 TCTATTCCATTACAGCGAACCAAACGCACTGTTATAGT
1 TCTATTCCATTACAGCGAACCAAACGCACTGTTATAGT
25696268 TCTATTCCATTACAGCGAACCAAACGCACTGTTATAGT
1 TCTATTCCATTACAGCGAACCAAACGCACTGTTATAGT
25696306 TCTATTCCATTACA
1 TCTATTCCATTACA
25696320 TTCAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (38 bp):
TCTATTCCATTACAGCGAACCAAACGCACTGTTATAGT
Found at i:25696364 original size:16 final size:16
Alignment explanation
Indices: 25696343--25696382 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
25696333 TTGAATTATT
25696343 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCA
*
25696359 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCA
25696375 ATTACAGC
1 ATTACAGC
25696383 GAACCAAACG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:25698480 original size:40 final size:37
Alignment explanation
Indices: 25698427--25698553 Score: 114
Period size: 42 Copynumber: 3.2 Consensus size: 37
25698417 TGGCCCGGCC
25698427 CAAAT-TATATATTAAATATATTTTTTTATTTTTAAT
1 CAAATATATATATTAAATATATTTTTTTATTTTTAAT
* *
25698463 CAAATATACTTTTTATTAAATATATATATTTTTTGGACTTTTAAT
1 CAAATATA---TATATT-AA-ATATAT-TTTTTT--ATTTTTAAT
*
25698508 CCGAAT-TATATATTAAATATATGTTTTTTTATTTTTAAT
1 -CAAATATATATATTAAATATA--TTTTTTTATTTTTAAT
25698547 CAAATAT
1 CAAATAT
25698554 GGGTCGGGCC
Statistics
Matches: 72, Mismatches: 6, Indels: 23
0.71 0.06 0.23
Matches are distributed among these distances:
36 5 0.07
37 2 0.03
38 4 0.06
39 9 0.12
40 10 0.14
41 10 0.14
42 12 0.17
43 6 0.08
45 10 0.14
46 4 0.06
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (37 bp):
CAAATATATATATTAAATATATTTTTTTATTTTTAAT
Found at i:25698496 original size:20 final size:20
Alignment explanation
Indices: 25698436--25698496 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
25698426 CCAAATTATA
25698436 TATTAAATATAT-T-TTTTT
1 TATTAAATATATATATTTTT
* * * *
25698454 ATTTTTAATCAAATATACTTTT
1 -TATTAAAT-ATATATATTTTT
25698476 TATTAAATATATATATTTTT
1 TATTAAATATATATATTTTT
25698496 T
1 T
25698497 GGACTTTTAA
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
19 6 0.19
20 14 0.45
21 7 0.23
22 4 0.13
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTAAATATATATATTTTT
Found at i:25699479 original size:20 final size:20
Alignment explanation
Indices: 25699429--25699467 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
25699419 TGGAGCAGGA
*
25699429 ATATCGATACCTTAGGAAAT
1 ATATCGATACCTTAAGAAAT
25699449 ATATCGATACCTTAAGAAA
1 ATATCGATACCTTAAGAAA
25699468 AGTATTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
ATATCGATACCTTAAGAAAT
Found at i:25699728 original size:58 final size:58
Alignment explanation
Indices: 25699658--25699776 Score: 229
Period size: 58 Copynumber: 2.1 Consensus size: 58
25699648 TCAGCTTTAC
25699658 TTTTATTCAAAAACACTTTAATTTATTATATCAAAACAAATAATCCAATAATGATTAG
1 TTTTATTCAAAAACACTTTAATTTATTATATCAAAACAAATAATCCAATAATGATTAG
*
25699716 TTTTATTCAAAAACACTTTAATTTATTATATCAAAACAGATAATCCAATAATGATTAG
1 TTTTATTCAAAAACACTTTAATTTATTATATCAAAACAAATAATCCAATAATGATTAG
25699774 TTT
1 TTT
25699777 AACATGTTTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (58 bp):
TTTTATTCAAAAACACTTTAATTTATTATATCAAAACAAATAATCCAATAATGATTAG
Found at i:25701024 original size:18 final size:18
Alignment explanation
Indices: 25700984--25701030 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
25700974 ACACCAATTT
*
25700984 GTTATTTGAACTATTCAA
1 GTTATTTGAATTATTCAA
* *
25701002 ATTATTTGAATTATTCAC
1 GTTATTTGAATTATTCAA
*
25701020 GTTATTCGAAT
1 GTTATTTGAAT
25701031 GGTTAAATTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (18 bp):
GTTATTTGAATTATTCAA
Found at i:25701273 original size:14 final size:14
Alignment explanation
Indices: 25701256--25701286 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
25701246 AGTAAAATAT
*
25701256 TTTCTGGAAAATGA
1 TTTCTAGAAAATGA
25701270 TTTCTAGAAAATGA
1 TTTCTAGAAAATGA
25701284 TTT
1 TTT
25701287 ACTTTTCTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.42
Consensus pattern (14 bp):
TTTCTAGAAAATGA
Found at i:25701302 original size:19 final size:19
Alignment explanation
Indices: 25701278--25701315 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
25701268 GATTTCTAGA
25701278 AAATGATTTACTTTTCTGG
1 AAATGATTTACTTTTCTGG
25701297 AAATGATTTACTTTTCTGG
1 AAATGATTTACTTTTCTGG
25701316 TGTTTGGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (19 bp):
AAATGATTTACTTTTCTGG
Found at i:25702888 original size:43 final size:43
Alignment explanation
Indices: 25702781--25703048 Score: 317
Period size: 43 Copynumber: 6.3 Consensus size: 43
25702771 TTATTTTTAT
* * **** *
25702781 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGC-ATTACGAAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCAAC
* *
25702823 AAATGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCAAC
* * *
25702866 AAACGCCGCTAAAGATCATGTTCCTTAGCGGCGTTTTTTCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCAAC
* *
25702909 AAACGCCTCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCAAC
* **
25702952 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCTTCCGC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCAAC
* * *
25702995 AAACGCCACTAAAGGTCATGTTCTTTTAGCGGC-ATTTTT-ACAC
1 AAACGCCGCTAAAGATCATGTTC-TTTAGCGGCGCTTTTTCA-AC
25703038 AAACGCCGCTA
1 AAACGCCGCTA
25703049 TTTGTTTGGT
Statistics
Matches: 198, Mismatches: 25, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
42 31 0.16
43 158 0.80
44 9 0.05
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCAAC
Found at i:25703169 original size:15 final size:15
Alignment explanation
Indices: 25703144--25703182 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
25703134 GCCCTCCTGT
25703144 AGCAA-CAAATCAAA
1 AGCAACCAAATCAAA
*
25703158 AGCAACCAAATCTAA
1 AGCAACCAAATCAAA
*
25703173 ACCAACCAAA
1 AGCAACCAAA
25703183 AGCAATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.59, C:0.28, G:0.05, T:0.08
Consensus pattern (15 bp):
AGCAACCAAATCAAA
Found at i:25703590 original size:87 final size:87
Alignment explanation
Indices: 25703423--25703581 Score: 228
Period size: 87 Copynumber: 1.8 Consensus size: 87
25703413 CGCTACAGCG
* * *
25703423 TCTGCTTCTCTCGATGCCGCATCTACTTTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTAAAC
1 TCTGCTTCCCTCGATGCCGCATCTACTTTAAGTTGTAGCTAGAGTTCTTCATATTTCCTTTAAAC
* *
25703488 CTCTACTTCTCTCGCTGCAACC
66 CTCAACTTCGCTCGCTGCAACC
* * ** *
25703510 TCTGCTTCCCTCGTTGCCGCCTCTGGTTTAAGTTGTAGCTAGAGTTCTTCATATTTCCTTTGAAC
1 TCTGCTTCCCTCGATGCCGCATCTACTTTAAGTTGTAGCTAGAGTTCTTCATATTTCCTTTAAAC
25703575 CTCAACT
66 CTCAACT
25703582 ATGGTCGCTT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 63 1.00
ACGTcount: A:0.16, C:0.28, G:0.15, T:0.40
Consensus pattern (87 bp):
TCTGCTTCCCTCGATGCCGCATCTACTTTAAGTTGTAGCTAGAGTTCTTCATATTTCCTTTAAAC
CTCAACTTCGCTCGCTGCAACC
Found at i:25709414 original size:34 final size:34
Alignment explanation
Indices: 25709341--25709417 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 34
25709331 NNNNNNNNNN
* * **
25709341 ATGTATTATGTAAGTTATGTAAGTTTTTGTTTTT
1 ATGTATTATGTAACTTATGTAAGTTTATGTGGTT
* *
25709375 GTGTATTATGTAACTTATTTAA-TTTATGTAGGTT
1 ATGTATTATGTAACTTATGTAAGTTTATGT-GGTT
25709409 ATGTATTAT
1 ATGTATTAT
25709418 TATGTAAGTT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
33 6 0.17
34 29 0.83
ACGTcount: A:0.26, C:0.01, G:0.17, T:0.56
Consensus pattern (34 bp):
ATGTATTATGTAACTTATGTAAGTTTATGTGGTT
Found at i:25709431 original size:12 final size:12
Alignment explanation
Indices: 25709414--25709458 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
25709404 AGGTTATGTA
25709414 TTATTATGTAAG
1 TTATTATGTAAG
*
25709426 TTATTATGTAGG
1 TTATTATGTAAG
25709438 TTATTATGTAAG
1 TTATTATGTAAG
*
25709450 TCATTATGT
1 TTATTATGT
25709459 TGGTTATGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.51
Consensus pattern (12 bp):
TTATTATGTAAG
Found at i:25709444 original size:24 final size:24
Alignment explanation
Indices: 25709407--25709465 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
25709397 TTTATGTAGG
*
25709407 TTATGTA--TTATTATGTAAGTTA
1 TTATGTAGGTTATTATGTAAGTCA
25709429 TTATGTAGGTTATTATGTAAGTCA
1 TTATGTAGGTTATTATGTAAGTCA
*
25709453 TTATGTTGGTTAT
1 TTATGTAGGTTAT
25709466 GTAAGTTGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 7 0.21
24 26 0.79
ACGTcount: A:0.27, C:0.02, G:0.19, T:0.53
Consensus pattern (24 bp):
TTATGTAGGTTATTATGTAAGTCA
Found at i:25709467 original size:21 final size:22
Alignment explanation
Indices: 25709417--25709471 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 22
25709407 TTATGTATTA
*
25709417 TTATGTAAGTTATTATGTAGGTT
1 TTATGTAAGTCATTATGTAGG-T
*
25709440 ATTATGTAAGTCATTATGTTGG-
1 -TTATGTAAGTCATTATGTAGGT
25709462 TTATGTAAGT
1 TTATGTAAGT
25709472 TGTGATATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 10 0.34
24 19 0.66
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (22 bp):
TTATGTAAGTCATTATGTAGGT
Found at i:25709618 original size:19 final size:19
Alignment explanation
Indices: 25709594--25709653 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
25709584 ATGTATCAAT
25709594 TTTTAAAAATATATATAAA
1 TTTTAAAAATATATATAAA
*
25709613 TTTTAAATATATATAT-AA
1 TTTTAAAAATATATATAAA
*
25709631 --TTAAAACTATATATAAA
1 TTTTAAAAATATATATAAA
*
25709648 TATTAA
1 TTTTAA
25709654 TAAGTTATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
16 12 0.34
17 2 0.06
18 2 0.06
19 19 0.54
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTTAAAAATATATATAAA
Found at i:25709641 original size:18 final size:17
Alignment explanation
Indices: 25709599--25709653 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 17
25709589 TCAATTTTTA
25709599 AAAATATATATAAATTT
1 AAAATATATATAAATTT
*
25709616 TAAATATATATATAA-TT
1 AAAATATATATA-AATTT
25709633 AAAACTATATATAAATATT
1 AAAA-TATATATAAAT-TT
25709652 AA
1 AA
25709654 TAAGTTATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 18 0.56
18 10 0.31
19 4 0.12
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATATATATAAATTT
Found at i:25709668 original size:9 final size:9
Alignment explanation
Indices: 25709654--25709733 Score: 69
Period size: 9 Copynumber: 9.0 Consensus size: 9
25709644 TAAATATTAA
25709654 TAAGTTATG
1 TAAGTTATG
25709663 TAAGTTATG
1 TAAGTTATG
* *
25709672 TATTA-TAAATT
1 TA--AGT-TATG
*
25709683 TAAATTATG
1 TAAGTTATG
25709692 TAAGTTATG
1 TAAGTTATG
25709701 -AA-TTATG
1 TAAGTTATG
25709708 TAAGTTATG
1 TAAGTTATG
*
25709717 TAA-TTACG
1 TAAGTTATG
25709725 TAAGTTATG
1 TAAGTTATG
25709734 AAATTTGAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
7 5 0.09
8 11 0.19
9 34 0.60
10 2 0.04
11 5 0.09
ACGTcount: A:0.38, C:0.01, G:0.16, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:25709727 original size:17 final size:16
Alignment explanation
Indices: 25709658--25709735 Score: 90
Period size: 16 Copynumber: 5.0 Consensus size: 16
25709648 TATTAATAAG
*
25709658 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGAA
* *
25709674 TTA--TAAATT-TAAA
1 TTATGTAAGTTATGAA
25709687 TTATGTAAGTTATGAA
1 TTATGTAAGTTATGAA
25709703 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATG-AA
*
25709720 TTACGTAAGTTATGAA
1 TTATGTAAGTTATGAA
25709736 ATTTGAACTT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
13 5 0.10
14 5 0.10
15 5 0.10
16 22 0.42
17 15 0.29
ACGTcount: A:0.38, C:0.01, G:0.15, T:0.45
Consensus pattern (16 bp):
TTATGTAAGTTATGAA
Found at i:25709738 original size:17 final size:17
Alignment explanation
Indices: 25709684--25709738 Score: 85
Period size: 17 Copynumber: 3.3 Consensus size: 17
25709674 TTATAAATTT
25709684 AAATTATGTAAGTTATG
1 AAATTATGTAAGTTATG
25709701 -AATTATGTAAGTTATG
1 AAATTATGTAAGTTATG
* *
25709717 TAATTACGTAAGTTATG
1 AAATTATGTAAGTTATG
25709734 AAATT
1 AAATT
25709739 TGAACTTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
16 16 0.46
17 19 0.54
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (17 bp):
AAATTATGTAAGTTATG
Found at i:25710528 original size:14 final size:14
Alignment explanation
Indices: 25710509--25710538 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
25710499 CTCGAACAGC
25710509 AAGATGATTAACTA
1 AAGATGATTAACTA
25710523 AAGATGATTAACTA
1 AAGATGATTAACTA
25710537 AA
1 AA
25710539 AAACCTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (14 bp):
AAGATGATTAACTA
Found at i:25713426 original size:15 final size:14
Alignment explanation
Indices: 25713406--25713437 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
25713396 CACTAACATC
25713406 TAACCCCTAAACCCT
1 TAACCCCTAAA-CCT
25713421 TAACCCCTAAACCT
1 TAACCCCTAAACCT
25713435 TAA
1 TAA
25713438 ATCCTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.22
Consensus pattern (14 bp):
TAACCCCTAAACCT
Found at i:25714368 original size:113 final size:114
Alignment explanation
Indices: 25714152--25714379 Score: 350
Period size: 113 Copynumber: 2.0 Consensus size: 114
25714142 TGTGCCTTGG
* * * * *
25714152 AGCCCTGAGCGTTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCCGAAAGCTTAGAAAACGG
1 AGCCCTGAGCATTAGCGGCGCTTTCCTAAAAACGCCGCTAAATCCCCCGAAAGCTCACAAAACGA
* * *
25714217 CGTCGTTGTGCTTAGGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAA
66 CATCGTTGGGCTTAGGTTTTTTGCGGCACTTTCTCAAAAACGCCGCTAA
25714266 AGCCCTGAGCATTAGCGGCGCTTTCCTAAAAACGCCGCTAAAT-CCCCGAAAGCTCACAAAACGA
1 AGCCCTGAGCATTAGCGGCGCTTTCCTAAAAACGCCGCTAAATCCCCCGAAAGCTCACAAAACGA
** *
25714330 CATCGTTGGGCTTATTTTTTTTGCGGCACTTTCTCAAAAACGCTGCTAA
66 CATCGTTGGGCTTAGGTTTTTTGCGGCACTTTCTCAAAAACGCCGCTAA
25714379 A
1 A
25714380 TCCCCGAAAG
Statistics
Matches: 103, Mismatches: 11, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
113 62 0.60
114 41 0.40
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (114 bp):
AGCCCTGAGCATTAGCGGCGCTTTCCTAAAAACGCCGCTAAATCCCCCGAAAGCTCACAAAACGA
CATCGTTGGGCTTAGGTTTTTTGCGGCACTTTCTCAAAAACGCCGCTAA
Found at i:25714369 original size:72 final size:72
Alignment explanation
Indices: 25714280--25714608 Score: 372
Period size: 72 Copynumber: 4.4 Consensus size: 72
25714270 CTGAGCATTA
* * *
25714280 GCGGCGCTTTC-CTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGACATCGTTGGGCTTA
1 GCGGCGCTTTCTC-AAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
25714344 TTTTTTTT
65 TTTTTTTT
* * * *
25714352 GCGGCACTTTCTCAAAAACGCTGCTAAATCCCCGAAAGCTCAGAAAACTGTGTCGTTGGGCTTAT
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA-
25714417 GTTTTTTTCACT
65 -TTTTTTT---T
* *
25714429 GAGCATTAGTGGCGCTTTCTTAAAAACACCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTT
1 --GC------GGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTT
25714494 GGGCTTATGTTTTTTT
58 GGGCTTAT-TTTTTTT
* * *
25714510 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTTAGAAAACGGTGTCGTTGGGCTTAG
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAT
*
25714575 GTTTTTT
66 TTTTTTT
** *
25714582 GCGGCGCTTTCTGGAAAACGACGCTAA
1 GCGGCGCTTTCTCAAAAACGCCGCTAA
25714609 TGCTTATTTT
Statistics
Matches: 220, Mismatches: 22, Indels: 30
0.81 0.08 0.11
Matches are distributed among these distances:
72 85 0.39
73 59 0.27
74 7 0.03
77 1 0.00
79 4 0.02
81 1 0.00
83 1 0.00
84 6 0.03
85 56 0.25
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (72 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAT
TTTTTTT
Found at i:25714558 original size:73 final size:72
Alignment explanation
Indices: 25714439--25714608 Score: 259
Period size: 73 Copynumber: 2.3 Consensus size: 72
25714429 GAGCATTAGT
* * *
25714439 GGCGCTTTCTTAAAAACACCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTATGT
1 GGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA-GG
25714504 TTTTTTGC
65 TTTTTTGC
* *
25714512 GGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTTAGAAAACGGTGTCGTTGGGCTTAGGT
1 GGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGT
25714577 TTTTTGC
66 TTTTTGC
** *
25714584 GGCGCTTTCTGGAAAACGACGCTAA
1 GGCGCTTTCTCAAAAACGCCGCTAA
25714609 TGCTTATTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
72 31 0.35
73 58 0.65
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (72 bp):
GGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGT
TTTTTGC
Found at i:25714580 original size:157 final size:157
Alignment explanation
Indices: 25714270--25714581 Score: 509
Period size: 157 Copynumber: 2.0 Consensus size: 157
25714260 CGCTAAAGCC
*
25714270 CTGAGCATTAGCGGCGCTTTCCTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGACATCG
1 CTGAGCATTAGCGGCGCTTTCCTAAAAACACCGCTAAATCCCCGAAAGCTCACAAAACGACATCG
*
25714335 TTGGGCTTATTTTTTTTGCGGCACTTTCTCAAAAACGCTGCTAAATCCCCGAAAGCTCAGAAAAC
66 TTGGGCTTATTTTTTTTGCGGCACTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
* *
25714400 TGTGTCGTTGGGCTTATGTTTTTTTCA
131 GGTGTCGTTGGGCTTATGGTTTTTTCA
* * * * *
25714427 CTGAGCATTAGTGGCGCTTTCTTAAAAACACCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCG
1 CTGAGCATTAGCGGCGCTTTCCTAAAAACACCGCTAAATCCCCGAAAGCTCACAAAACGACATCG
* *
25714492 TTGGGCTTATGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTTAGAAAA
66 TTGGGCTTAT-TTTTTTTGCGGCACTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAA
25714557 CGGTGTCGTTGGGCTTA-GGTTTTTT
130 CGGTGTCGTTGGGCTTATGGTTTTTT
25714582 GCGGCGCTTT
Statistics
Matches: 143, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
157 76 0.53
158 67 0.47
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.29
Consensus pattern (157 bp):
CTGAGCATTAGCGGCGCTTTCCTAAAAACACCGCTAAATCCCCGAAAGCTCACAAAACGACATCG
TTGGGCTTATTTTTTTTGCGGCACTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
GGTGTCGTTGGGCTTATGGTTTTTTCA
Found at i:25715954 original size:18 final size:18
Alignment explanation
Indices: 25715914--25715956 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
25715904 AATTTAAACC
25715914 TATAATAAAATTGTTAAA
1 TATAATAAAATTGTTAAA
* *
25715932 AATAATAATATTG-TAATA
1 TATAATAAAATTGTTAA-A
25715950 TATAATA
1 TATAATA
25715957 TATGTTAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (18 bp):
TATAATAAAATTGTTAAA
Found at i:25716461 original size:4 final size:4
Alignment explanation
Indices: 25716445--25716486 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
25716435 CAGTTCGCTT
25716445 TGTC TGT- TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGT
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGT
25716487 TTGTTTGTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.08
4 34 0.92
ACGTcount: A:0.00, C:0.21, G:0.26, T:0.52
Consensus pattern (4 bp):
TGTC
Found at i:25716979 original size:16 final size:18
Alignment explanation
Indices: 25716948--25716986 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
25716938 GATTATGTGA
25716948 TTGTGTCAACATTTATGC
1 TTGTGTCAACATTTATGC
*
25716966 TTGTG-CAA-ATTTATGT
1 TTGTGTCAACATTTATGC
25716982 TTGTG
1 TTGTG
25716987 GAGAATGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.49
Consensus pattern (18 bp):
TTGTGTCAACATTTATGC
Found at i:25719136 original size:26 final size:26
Alignment explanation
Indices: 25719107--25719158 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
25719097 TTTAGTTTCC
**
25719107 TTAATTATAGTTTCTTTTTCTACAAG
1 TTAATTATAGTTTCTTAGTCTACAAG
*
25719133 TTAATTTTAGTTTCTTAGTCTACAAG
1 TTAATTATAGTTTCTTAGTCTACAAG
25719159 AATAAAATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.52
Consensus pattern (26 bp):
TTAATTATAGTTTCTTAGTCTACAAG
Found at i:25726015 original size:32 final size:32
Alignment explanation
Indices: 25725969--25726033 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
25725959 TAAGGGGGAG
25725969 TGTTGAAATCCCTATAATTAAGGATAGAAATC
1 TGTTGAAATCCCTATAATTAAGGATAGAAATC
* *
25726001 TGTTGGAATTCCTATAATTAAGGATAGAAATC
1 TGTTGAAATCCCTATAATTAAGGATAGAAATC
25726033 T
1 T
25726034 TACCTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (32 bp):
TGTTGAAATCCCTATAATTAAGGATAGAAATC
Found at i:25731000 original size:19 final size:18
Alignment explanation
Indices: 25730956--25731037 Score: 85
Period size: 19 Copynumber: 4.3 Consensus size: 18
25730946 AATTACAAAA
25730956 AAAATATTCAAAATAAATTTT
1 AAAA-ATTCAAAAT--ATTTT
25730977 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTT-T
* *
25730996 AAAAATTTAAAA-ATTAT
1 AAAAATTCAAAATATTTT
*
25731013 AAAAATTCTAAAAAATTTT
1 AAAAATTC-AAAATATTTT
25731032 AAAAAT
1 AAAAAT
25731038 ATATATAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
17 8 0.15
18 11 0.20
19 22 0.41
20 9 0.17
21 4 0.07
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAAATTCAAAATATTTT
Found at i:25731017 original size:10 final size:9
Alignment explanation
Indices: 25730970--25731047 Score: 61
Period size: 9 Copynumber: 8.3 Consensus size: 9
25730960 TATTCAAAAT
*
25730970 AAATTTTAA
1 AAATTATAA
25730979 AAATTCA-AA
1 AAATT-ATAA
*
25730988 ATATTTATAA
1 A-AATTATAA
25730998 AAATT-TAA
1 AAATTATAA
25731006 AAATTATAA
1 AAATTATAA
*
25731015 AAATTCTAAA
1 AAATTAT-AA
*
25731025 AAATTTTAA
1 AAATTATAA
25731034 AAATATATATA
1 AAAT-TATA-A
25731045 AAA
1 AAA
25731048 AAAGGTTCAA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
8 8 0.14
9 27 0.48
10 17 0.30
11 4 0.07
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (9 bp):
AAATTATAA
Found at i:25731040 original size:27 final size:28
Alignment explanation
Indices: 25730956--25731040 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 28
25730946 AATTACAAAA
*
25730956 AAAATATTCAAAATAAATTTTAAAAAT-T
1 AAAATATTCTAAA-AAATTTTAAAAATAT
25730984 CAAAATATT-TATAAAAA-TTTAAAAATTAT
1 -AAAATATTCTA-AAAAATTTTAAAAA-TAT
25731013 AAAA-ATTCTAAAAAATTTTAAAAATAT
1 AAAATATTCTAAAAAATTTTAAAAATAT
25731040 A
1 A
25731041 TATAAAAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
27 20 0.40
28 19 0.38
29 11 0.22
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (28 bp):
AAAATATTCTAAAAAATTTTAAAAATAT
Found at i:25731421 original size:16 final size:16
Alignment explanation
Indices: 25731400--25731434 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
25731390 TCGATCGAAC
25731400 TCTCACCCTGATTACA
1 TCTCACCCTGATTACA
*
25731416 TCTCACGCTGATTACA
1 TCTCACCCTGATTACA
25731432 TCT
1 TCT
25731435 AAGGTCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.23, C:0.34, G:0.09, T:0.34
Consensus pattern (16 bp):
TCTCACCCTGATTACA
Found at i:25735801 original size:8 final size:8
Alignment explanation
Indices: 25735788--25735814 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
25735778 TTAACTAGTT
25735788 TAATTAAC
1 TAATTAAC
25735796 TAATTAAC
1 TAATTAAC
25735804 TAATTAAC
1 TAATTAAC
25735812 TAA
1 TAA
25735815 CTAGACCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (8 bp):
TAATTAAC
Found at i:25738665 original size:13 final size:13
Alignment explanation
Indices: 25738647--25738672 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25738637 TAGTTTATCG
25738647 AAATTATTATAAT
1 AAATTATTATAAT
25738660 AAATTATTATAAT
1 AAATTATTATAAT
25738673 TATGATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATTATTATAAT
Found at i:25740778 original size:13 final size:13
Alignment explanation
Indices: 25740749--25740825 Score: 64
Period size: 13 Copynumber: 5.9 Consensus size: 13
25740739 CAAGCATGGA
**
25740749 GCTAAGTGATATG
1 GCTAAGTGATACC
*
25740762 GCTAAGTGGTACC
1 GCTAAGTGATACC
* * *
25740775 GCTAAGGGGTGCC
1 GCTAAGTGATACC
* *
25740788 ACTAAGTGATACT
1 GCTAAGTGATACC
*
25740801 GCTAAGTGACACC
1 GCTAAGTGATACC
*
25740814 GCTAAGTAATAC
1 GCTAAGTGATAC
25740826 TGCGAAATGG
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 49 1.00
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.23
Consensus pattern (13 bp):
GCTAAGTGATACC
Found at i:25746623 original size:29 final size:30
Alignment explanation
Indices: 25746581--25746661 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
25746571 GAATTTGATC
* **
25746581 AAATCAAAATTTCATGTATAAAATTGTACA-
1 AAATC-AAAGTTCATGTATAAAATTACACAT
*
25746611 AAATCAAAGTTCATGTATACAATTACACATT
1 AAATCAAAGTTCATGTATAAAATTACACA-T
* *
25746642 AAACCATAGTTCATGTATAA
1 AAATCAAAGTTCATGTATAA
25746662 TTTTGAGATA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 20 0.48
30 5 0.12
31 17 0.40
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.32
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATTACACAT
Found at i:25747777 original size:7 final size:7
Alignment explanation
Indices: 25747765--25747803 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
25747755 TTTTCTGATT
25747765 CTTTATC
1 CTTTATC
25747772 CTTTATC
1 CTTTATC
25747779 CTTTATC
1 CTTTATC
25747786 CTTTATC
1 CTTTATC
25747793 CTTTATC
1 CTTTATC
25747800 CTTT
1 CTTT
25747804 TCTTTTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.13, C:0.28, G:0.00, T:0.59
Consensus pattern (7 bp):
CTTTATC
Found at i:25747938 original size:23 final size:22
Alignment explanation
Indices: 25747889--25747966 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
25747879 TTATTATTGG
* * *
25747889 TTTTATAAAATTTGAAATGTACA
1 TTTT-TAAAATTTTAAATATATA
*
25747912 -TTTTAAATGTTTTATAATAT-TA
1 TTTTTAAA-ATTTTA-AATATATA
25747934 TTTTTAAAATTTTAAATATATA
1 TTTTTAAAATTTTAAATATATA
25747956 TTTTTAAAATT
1 TTTTTAAAATT
25747967 ATTTTTTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
21 9 0.20
22 26 0.57
23 11 0.24
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (22 bp):
TTTTTAAAATTTTAAATATATA
Found at i:25747972 original size:13 final size:14
Alignment explanation
Indices: 25747943--25747979 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
25747933 ATTTTTAAAA
25747943 TTTT-AAATATATAT
1 TTTTAAAAT-TATAT
25747957 TTTTAAAATTAT-T
1 TTTTAAAATTATAT
25747970 TTTTAAAATT
1 TTTTAAAATT
25747980 TAAATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.50
14 7 0.32
15 4 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTAAAATTATAT
Found at i:25747972 original size:34 final size:34
Alignment explanation
Indices: 25747921--25747992 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
25747911 ATTTTAAATG
*
25747921 TTTTATAATATTA-TTTTTAAAATTTTAAATATATA
1 TTTTATAAAATTATTTTTTAAAA-TTTAAAT-TATA
*
25747956 TTTT-TAAAATTATTTTTTAAAATTTAAATTTTA
1 TTTTATAAAATTATTTTTTAAAATTTAAATTATA
25747989 TTTT
1 TTTT
25747993 CAAATTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 7 0.21
34 14 0.41
35 13 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (34 bp):
TTTTATAAAATTATTTTTTAAAATTTAAATTATA
Found at i:25747983 original size:20 final size:20
Alignment explanation
Indices: 25747958--25748026 Score: 61
Period size: 22 Copynumber: 3.4 Consensus size: 20
25747948 AATATATATT
25747958 TTTAAAATTATTTTTTAAAA
1 TTTAAAATTATTTTTTAAAA
*
25747978 TTT-AAATT-TTATTTTCAAAT
1 TTTAAAATTATT-TTTT-AAAA
* *
25747998 TTTAAATATAATTTTTTAATA
1 TTTAAA-ATTATTTTTTAAAA
25748019 TTCTAAAA
1 TT-TAAAA
25748027 CATTTAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
18 2 0.05
19 9 0.23
20 9 0.23
21 7 0.18
22 10 0.26
23 2 0.05
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTAAAATTATTTTTTAAAA
Found at i:25754166 original size:21 final size:21
Alignment explanation
Indices: 25754142--25754195 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
25754132 TGACCAATTA
25754142 TAATATATATTTTTAATTTTC
1 TAATATATATTTTTAATTTTC
* * *
25754163 TAATATAAATTTTTACTTTTT
1 TAATATATATTTTTAATTTTC
25754184 TAATATATATTT
1 TAATATATATTT
25754196 AAAAAAGTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
TAATATATATTTTTAATTTTC
Found at i:25754232 original size:20 final size:20
Alignment explanation
Indices: 25754208--25754253 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
25754198 AAAAGTCATA
25754208 ATTTTTTTAACAAATAAAT-
1 ATTTTTTTAACAAATAAATC
*
25754227 ATTTTTTTAATAAATAAATC
1 ATTTTTTTAACAAATAAATC
25754247 ATTTTTT
1 ATTTTTT
25754254 ATTTTTTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTTTTTAACAAATAAATC
Found at i:25754290 original size:24 final size:23
Alignment explanation
Indices: 25754237--25754292 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
25754227 ATTTTTTTAA
* * *
25754237 TAAATAAATCATTTTTTATTTTT
1 TAAATAAATCAATTTTCACTTTT
*
25754260 TCCAATAAACTCAATTTTCACTTTT
1 T-AAATAAA-TCAATTTTCACTTTT
25754285 TAAATAAA
1 TAAATAAA
25754293 ATATTATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 1 0.04
24 12 0.46
25 13 0.50
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.48
Consensus pattern (23 bp):
TAAATAAATCAATTTTCACTTTT
Found at i:25754369 original size:15 final size:15
Alignment explanation
Indices: 25754349--25754388 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
25754339 ATCTTTAAAA
*
25754349 ATAATTTTAAAAATC
1 ATAATTTAAAAAATC
*
25754364 ATAATTTAAAAAATT
1 ATAATTTAAAAAATC
25754379 AT-ATTTAAAA
1 ATAATTTAAAA
25754389 TTAAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATTTAAAAAATC
Found at i:25754390 original size:21 final size:23
Alignment explanation
Indices: 25754366--25754459 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 23
25754356 TAAAAATCAT
25754366 AATTTAAAAAAT-TATATTT-AA
1 AATTTAAAAAATATATATTTAAA
*
25754387 AA-TTAAATAAATATATTTTTAAA
1 AATTTAAA-AAATATATATTTAAA
* * *
25754410 AATTT-TAAAATATACATTAAAA
1 AATTTAAAAAATATATATTTAAA
*
25754432 ATATTATAAAAAAATAATAAATTTAAA
1 A-ATT-T-AAAAAAT-ATATATTTAAA
25754459 A
1 A
25754460 GGTCATATCT
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
20 5 0.09
21 6 0.11
22 19 0.34
23 8 0.14
24 3 0.05
26 5 0.09
27 10 0.18
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (23 bp):
AATTTAAAAAATATATATTTAAA
Found at i:25754488 original size:16 final size:16
Alignment explanation
Indices: 25754464--25754522 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
25754454 TTAAAAGGTC
25754464 ATATCTTTAAAAATAAT
1 ATAT-TTTAAAAATAAT
** **
25754481 ATATTTTAAATGTTTT
1 ATATTTTAAAAATAAT
25754497 ATATTATTAAAAA-AAT
1 ATATT-TTAAAAATAAT
25754513 ATA-TTTAAAA
1 ATATTTTAAAA
25754523 TTTTATAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
14 6 0.18
15 1 0.03
16 17 0.52
17 9 0.27
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (16 bp):
ATATTTTAAAAATAAT
Found at i:25754573 original size:21 final size:21
Alignment explanation
Indices: 25754538--25754599 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 21
25754528 TAAAACCAAT
* *
25754538 AATAAAAAAA-ATAAAAGACA
1 AATAAAAAAACTTAAAAAACA
*
25754558 AATAAAAAAACTTAAAAAATA
1 AATAAAAAAACTTAAAAAACA
25754579 AATAAAGAAGAAACTTAAAAA
1 AAT-AA-AA-AAACTTAAAAA
25754600 GAAAAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 10 0.29
21 10 0.29
22 2 0.06
23 2 0.06
24 11 0.31
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.15
Consensus pattern (21 bp):
AATAAAAAAACTTAAAAAACA
Found at i:25756189 original size:30 final size:30
Alignment explanation
Indices: 25756155--25756224 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
25756145 TTAAAATTTT
* * *
25756155 TCTTAACAATAATTCTAAAAAAATAAAAAA
1 TCTTAAAAATAAATATAAAAAAATAAAAAA
*
25756185 TCTTAAAAATAAATATAAAATAATAAAAATA
1 TCTTAAAAATAAATATAAAAAAATAAAAA-A
*
25756216 TATTAAAAA
1 TCTTAAAAA
25756225 GTATGTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 25 0.74
31 9 0.26
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (30 bp):
TCTTAAAAATAAATATAAAAAAATAAAAAA
Found at i:25756204 original size:20 final size:20
Alignment explanation
Indices: 25756171--25756215 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
25756161 CAATAATTCT
**
25756171 AAAA-AAATAAAAAATCTTA
1 AAAATAAATAAAAAATAATA
*
25756190 AAAATAAATATAAAATAATA
1 AAAATAAATAAAAAATAATA
25756210 AAAATA
1 AAAATA
25756216 TATTAAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAATAAATAAAAAATAATA
Found at i:25756275 original size:15 final size:15
Alignment explanation
Indices: 25756237--25756278 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
25756227 ATGTTAAACT
25756237 ATTTTTAAAAATAAA
1 ATTTTTAAAAATAAA
* *
25756252 AATTATAAATAA-AAA
1 ATTTTTAAA-AATAAA
25756267 ATTTTTAAAAAT
1 ATTTTTAAAAAT
25756279 TATAAATACA
Statistics
Matches: 21, Mismatches: 4, Indels: 4
0.72 0.14 0.14
Matches are distributed among these distances:
14 2 0.10
15 17 0.81
16 2 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTTTTAAAAATAAA
Found at i:25762441 original size:17 final size:17
Alignment explanation
Indices: 25762416--25762515 Score: 69
Period size: 17 Copynumber: 5.6 Consensus size: 17
25762406 AATCTTAGAG
25762416 TTCTAATTGTATACAAC
1 TTCTAATTGTATACAAC
* * *
25762433 TTTTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--A-AC
*
25762452 TTCTAATTGTATATAAC
1 TTCTAATTGTATACAAC
* *
25762469 TTCTAATTGTGT-CTTAGAG
1 TTCTAATTGTATAC--A-AC
25762488 TTCTAATTGTATACAAC
1 TTCTAATTGTATACAAC
*
25762505 TTTTAATTGTA
1 TTCTAATTGTA
25762516 GCCCTTGATG
Statistics
Matches: 62, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
16 1 0.02
17 33 0.53
18 4 0.06
19 23 0.37
20 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.48
Consensus pattern (17 bp):
TTCTAATTGTATACAAC
Found at i:25762455 original size:36 final size:36
Alignment explanation
Indices: 25762408--25762514 Score: 196
Period size: 36 Copynumber: 3.0 Consensus size: 36
25762398 GATTATGTAA
25762408 TCTTAGAGTTCTAATTGTATACAACTTTTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAACTTTTAATTGTG
* *
25762444 TCTTAGAGTTCTAATTGTATATAACTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAACTTTTAATTGTG
25762480 TCTTAGAGTTCTAATTGTATACAACTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAACTTTTAATTGT
25762515 AGCCCTTGAT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAACTTTTAATTGTG
Found at i:25762460 original size:19 final size:19
Alignment explanation
Indices: 25762436--25762497 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
25762426 ATACAACTTT
25762436 TAATTGTGTCTTAGAGTTC
1 TAATTGTGTCTTAGAGTTC
* * *
25762455 TAATTGTAT-ATA-ACTTC
1 TAATTGTGTCTTAGAGTTC
25762472 TAATTGTGTCTTAGAGTTC
1 TAATTGTGTCTTAGAGTTC
25762491 TAATTGT
1 TAATTGT
25762498 ATACAACTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 12 0.34
18 4 0.11
19 19 0.54
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.48
Consensus pattern (19 bp):
TAATTGTGTCTTAGAGTTC
Found at i:25763820 original size:5 final size:6
Alignment explanation
Indices: 25763782--25763833 Score: 76
Period size: 6 Copynumber: 9.3 Consensus size: 6
25763772 CAAAATAGTT
25763782 CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCC-CA CCC-CA CCC-CA
1 CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA CCCTCA
25763827 CCC-CA CC
1 CCCTCA CC
25763834 GCAAATACGA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 19 0.41
6 27 0.59
ACGTcount: A:0.17, C:0.73, G:0.00, T:0.10
Consensus pattern (6 bp):
CCCTCA
Found at i:25767127 original size:20 final size:20
Alignment explanation
Indices: 25767102--25767141 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
25767092 GATTAATTTT
25767102 TTTTATGAACTTTTTAAAAA
1 TTTTATGAACTTTTTAAAAA
** *
25767122 TTTTATTTATTTTTTAAAAA
1 TTTTATGAACTTTTTAAAAA
25767142 AAGTTTGAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTTATGAACTTTTTAAAAA
Found at i:25786566 original size:8 final size:8
Alignment explanation
Indices: 25786553--25786608 Score: 53
Period size: 8 Copynumber: 6.8 Consensus size: 8
25786543 ATTTATTTGA
25786553 AATATAAT
1 AATATAAT
25786561 AATATAAT
1 AATATAAT
*
25786569 -ATA-ATT
1 AATATAAT
25786575 AATATAATTT
1 AATATAA--T
25786585 ACAATATAAT
1 --AATATAAT
25786595 AATATAAT
1 AATATAAT
25786603 AATATA
1 AATATA
25786609 CTTAAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
6 2 0.05
7 6 0.15
8 23 0.57
10 2 0.05
12 7 0.17
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (8 bp):
AATATAAT
Found at i:25792702 original size:12 final size:12
Alignment explanation
Indices: 25792673--25792706 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
25792663 TGACCACGGA
25792673 AGAAAGGAAAAT
1 AGAAAGGAAAAT
*
25792685 -GAAAGGAAACT
1 AGAAAGGAAAAT
25792696 AGAAAGGAAAA
1 AGAAAGGAAAA
25792707 AGAGAGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.65, C:0.03, G:0.26, T:0.06
Consensus pattern (12 bp):
AGAAAGGAAAAT
Found at i:25797158 original size:40 final size:40
Alignment explanation
Indices: 25797114--25797264 Score: 189
Period size: 40 Copynumber: 3.8 Consensus size: 40
25797104 TCCATAATAT
*
25797114 TGGCAGTTTATCTCCATTACTAGTGGCTTGTCCACATTTC
1 TGGCAGTTTATCTCCATTACTGGTGGCTTGTCCACATTTC
*
25797154 TGGCAGTTTATCTACATTACTGGTGGCTTGTCCACATTAT-
1 TGGCAGTTTATCTCCATTACTGGTGGCTTGTCCACATT-TC
* * * * * *
25797194 TAGCAGCTTGTCTGCAATT-CTGGTGGTTTGTCCATATTTC
1 TGGCAGTTTATCT-CCATTACTGGTGGCTTGTCCACATTTC
*
25797234 TGGCAGTTTATCTGCATTACTGGTGGCTTGT
1 TGGCAGTTTATCTCCATTACTGGTGGCTTGT
25797265 TCGCAAACTA
Statistics
Matches: 92, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
39 4 0.04
40 84 0.91
41 4 0.04
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.41
Consensus pattern (40 bp):
TGGCAGTTTATCTCCATTACTGGTGGCTTGTCCACATTTC
Found at i:25797190 original size:20 final size:20
Alignment explanation
Indices: 25797128--25797192 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
25797118 AGTTTATCTC
*
25797128 CATTACTAGTGGCTTGTCCA
1 CATTACTGGTGGCTTGTCCA
* ** * * *
25797148 CATTTCTGGCAGTTTATCTA
1 CATTACTGGTGGCTTGTCCA
25797168 CATTACTGGTGGCTTGTCCA
1 CATTACTGGTGGCTTGTCCA
25797188 CATTA
1 CATTA
25797193 TTAGCAGCTT
Statistics
Matches: 32, Mismatches: 13, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.38
Consensus pattern (20 bp):
CATTACTGGTGGCTTGTCCA
Found at i:25805898 original size:29 final size:29
Alignment explanation
Indices: 25805854--25805919 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
25805844 ATTTGACCTT
* *
25805854 ATTGATTCTTTTTAATAATATAGAGACTAA
1 ATTGA-TCTATTTAATAATAGAGAGACTAA
*
25805884 ATTGATCTATTTAATAATAGAGGGACTAA
1 ATTGATCTATTTAATAATAGAGAGACTAA
*
25805913 TTTGATC
1 ATTGATC
25805920 CGGTCTCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 27 0.84
30 5 0.16
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.41
Consensus pattern (29 bp):
ATTGATCTATTTAATAATAGAGAGACTAA
Found at i:25809522 original size:20 final size:20
Alignment explanation
Indices: 25809497--25809539 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
25809487 ATCATAAAAA
25809497 TATTTTTTGATTATAGGATT
1 TATTTTTTGATTATAGGATT
25809517 TATTTTTTGATTATAGGATT
1 TATTTTTTGATTATAGGATT
25809537 TAT
1 TAT
25809540 CACTCACCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (20 bp):
TATTTTTTGATTATAGGATT
Found at i:25812897 original size:29 final size:29
Alignment explanation
Indices: 25812837--25812896 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
25812827 TATATATTCT
*
25812837 AAACCTAATCTAAAAATGAAAAGAAAATA
1 AAACCTAACCTAAAAATGAAAAGAAAATA
* * *
25812866 AAACGTAACCTAAAACTGAGAA-AAAATA
1 AAACCTAACCTAAAAATGAAAAGAAAATA
25812894 AAA
1 AAA
25812897 AGAAATGTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.65, C:0.12, G:0.08, T:0.15
Consensus pattern (29 bp):
AAACCTAACCTAAAAATGAAAAGAAAATA
Found at i:25816133 original size:20 final size:20
Alignment explanation
Indices: 25816099--25816151 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
25816089 AAGCCCCATG
* **
25816099 GTATTGATA-TTTTACACGA
1 GTATCGATATTTTTACAAAA
25816118 GTATCGATATTTTTACAAAA
1 GTATCGATATTTTTACAAAA
*
25816138 GTACCGATATTTTT
1 GTATCGATATTTTT
25816152 TAGTTGGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.43
Consensus pattern (20 bp):
GTATCGATATTTTTACAAAA
Found at i:25828549 original size:19 final size:19
Alignment explanation
Indices: 25828511--25828549 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
25828501 TTTAAGGAAA
*
25828511 ATGGTTACATAATTTGCAT
1 ATGGTTACATAATATGCAT
25828530 ATGGTTAGCATAATAT-CAT
1 ATGGTTA-CATAATATGCAT
25828549 A
1 A
25828550 AAAGTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (19 bp):
ATGGTTACATAATATGCAT
Found at i:25831761 original size:25 final size:26
Alignment explanation
Indices: 25831727--25831793 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
25831717 CCTTTTCATA
*
25831727 TATGCTCACATGAGCTGTG-AATAAG
1 TATGCTCACACGAGCTGTGAAATAAG
*
25831752 TATGCTCACACGAGCTGTGAAATGAG
1 TATGCTCACACGAGCTGTGAAATAAG
*
25831778 TCTGCTCACACGAGCT
1 TATGCTCACACGAGCT
25831794 TTGGTTCGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
25 18 0.47
26 20 0.53
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.25
Consensus pattern (26 bp):
TATGCTCACACGAGCTGTGAAATAAG
Found at i:25845709 original size:18 final size:18
Alignment explanation
Indices: 25845670--25845710 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
25845660 TGAAGTTCAG
* *
25845670 TTTTTAGATTTTTACAGG
1 TTTTTAGATTTTAACAGA
*
25845688 TTTTTAGATTTTAAGAGA
1 TTTTTAGATTTTAACAGA
25845706 TTTTT
1 TTTTT
25845711 TATAAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.15, T:0.59
Consensus pattern (18 bp):
TTTTTAGATTTTAACAGA
Found at i:25846390 original size:10 final size:10
Alignment explanation
Indices: 25846348--25846419 Score: 53
Period size: 10 Copynumber: 7.3 Consensus size: 10
25846338 ACTTCATACT
25846348 ATTTTTTA-A
1 ATTTTTTATA
*
25846357 ACTTTTTATAA
1 ATTTTTTAT-A
25846368 ATTTTTTATA
1 ATTTTTTATA
25846378 ATTTTTT-TGA
1 ATTTTTTAT-A
**
25846388 ATTTTAAATA
1 ATTTTTTATA
*
25846398 TTCTTTTTAT-
1 AT-TTTTTATA
25846408 A-TTTTTATA
1 ATTTTTTATA
25846417 ATT
1 ATT
25846420 ATTTGTTGAC
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
8 7 0.15
9 9 0.19
10 17 0.35
11 15 0.31
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:25849027 original size:43 final size:42
Alignment explanation
Indices: 25848926--25849127 Score: 343
Period size: 42 Copynumber: 4.8 Consensus size: 42
25848916 GTTTACAAAC
*
25848926 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
*
25848968 AAAAACGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG-AA
*
25849011 AAAAACGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* *
25849053 AAAAACGCCACTAAAAACCATGTTCTTTAGCGGCGCTTAG-A
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
25849094 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGC
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGC
25849128 ACTTTTATAC
Statistics
Matches: 153, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
41 33 0.22
42 78 0.51
43 42 0.27
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
Found at i:25849150 original size:85 final size:84
Alignment explanation
Indices: 25848926--25849127 Score: 352
Period size: 85 Copynumber: 2.4 Consensus size: 84
25848916 GTTTACAAAC
* * *
25848926 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCTCTAAAGACCATGT
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCACTAAAAACCATGT
25848991 TCTTTAGCGGCGCTTAGAAA
66 TCTTTAGCGGCGCTTAG-AA
*
25849011 AAAAACGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCACTAAAAACCATGT
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCACTAAAAACCATGT
25849076 TCTTTAGCGGCGCTTAG-A
66 TCTTTAGCGGCGCTTAGAA
25849094 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGC
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGC
25849128 ACTTTTATAC
Statistics
Matches: 112, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
83 34 0.30
85 78 0.70
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (84 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCACTAAAAACCATGT
TCTTTAGCGGCGCTTAGAA
Found at i:25855926 original size:50 final size:48
Alignment explanation
Indices: 25855872--25855993 Score: 122
Period size: 52 Copynumber: 2.4 Consensus size: 48
25855862 TAAGTCATGT
* *
25855872 AAAATATACTTAAAAATATATA-T-TTAAGTAATGTAAGATATAAGTTTTAA
1 AAAATATACTTAAAAATATATATTATTAA-TAATGTAA-AT-TAAATTGT-A
*
25855922 AAAATTATTACTTAAGAATATATATATTATTAATAATTTAAATTAAATTGTA
1 AAAA-TA-TACTTAA-AA-ATATATATTATTAATAATGTAAATTAAATTGTA
*
25855974 AAAATATATTTAAAAATATA
1 AAAATATACTTAAAAATATA
25855994 ATAAATATTG
Statistics
Matches: 62, Mismatches: 4, Indels: 14
0.77 0.05 0.17
Matches are distributed among these distances:
48 5 0.08
49 2 0.03
50 10 0.16
51 4 0.06
52 12 0.19
53 8 0.13
54 9 0.15
55 8 0.13
56 4 0.06
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (48 bp):
AAAATATACTTAAAAATATATATTATTAATAATGTAAATTAAATTGTA
Found at i:25856158 original size:13 final size:13
Alignment explanation
Indices: 25856111--25856160 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
25856101 CAAATTTTAG
*
25856111 TAAGTAATGTATT
1 TAAGTAATATATT
25856124 TAAGTAA-ATTATT
1 TAAGTAATA-TATT
25856137 TAAGTAATATATT
1 TAAGTAATATATT
*
25856150 CAAGTAATATA
1 TAAGTAATATA
25856161 ATAAAGTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 32 0.97
14 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (13 bp):
TAAGTAATATATT
Found at i:25856167 original size:26 final size:26
Alignment explanation
Indices: 25856112--25856169 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
25856102 AAATTTTAGT
* * * *
25856112 AAGTAATGTATTTAAGTAAATTATTT
1 AAGTAATATATTCAAGTAAATTAATA
25856138 AAGTAATATATTCAAGT-AATATAATA
1 AAGTAATATATTCAAGTAAAT-TAATA
25856164 AAGTAA
1 AAGTAA
25856170 ATTTTAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (26 bp):
AAGTAATATATTCAAGTAAATTAATA
Found at i:25856459 original size:67 final size:67
Alignment explanation
Indices: 25856387--25856517 Score: 253
Period size: 67 Copynumber: 2.0 Consensus size: 67
25856377 GAATCCCCTC
*
25856387 TATAATGAATTTATTAAACATTCAATCAATTAACTAACCAAAATTGATAATTCATTGACATTCAT
1 TATAATGAATTTATTAAACATTCAATCAATTAACTAACCAAAATTGAAAATTCATTGACATTCAT
25856452 TA
66 TA
25856454 TATAATGAATTTATTAAACATTCAATCAATTAACTAACCAAAATTGAAAATTCATTGACATTCA
1 TATAATGAATTTATTAAACATTCAATCAATTAACTAACCAAAATTGAAAATTCATTGACATTCA
25856518 ATCAATTAAT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.36
Consensus pattern (67 bp):
TATAATGAATTTATTAAACATTCAATCAATTAACTAACCAAAATTGAAAATTCATTGACATTCAT
TA
Found at i:25856598 original size:16 final size:16
Alignment explanation
Indices: 25856577--25856612 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
25856567 ATTAATTGAA
*
25856577 ATAAAATTGTAAATCG
1 ATAAAATTGCAAATCG
25856593 ATAAAATTGCAAATCG
1 ATAAAATTGCAAATCG
25856609 ATAA
1 ATAA
25856613 TTATAAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (16 bp):
ATAAAATTGCAAATCG
Found at i:25856683 original size:10 final size:10
Alignment explanation
Indices: 25856653--25856691 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
25856643 TTCGAATAAT
25856653 TATAAAATTA
1 TATAAAATTA
*
25856663 AATAAAATTA
1 TATAAAATTA
25856673 TATAAAATTA
1 TATAAAATTA
*
25856683 TTTAAAATT
1 TATAAAATT
25856692 TACCCATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TATAAAATTA
Found at i:25858831 original size:7 final size:7
Alignment explanation
Indices: 25858821--25858886 Score: 87
Period size: 7 Copynumber: 9.3 Consensus size: 7
25858811 ACCTCAAAAA
25858821 CCAAACC
1 CCAAACC
25858828 CCAAACC
1 CCAAACC
* *
25858835 CTAAACA
1 CCAAACC
*
25858842 CTAAACC
1 CCAAACC
25858849 CCAAACC
1 CCAAACC
25858856 CCAAACC
1 CCAAACC
*
25858863 CTAAACC
1 CCAAACC
25858870 CCAAACC
1 CCAAACC
25858877 CCAAAACC
1 CC-AAACC
25858885 CC
1 CC
25858887 GAACAGTAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
7 45 0.87
8 7 0.13
ACGTcount: A:0.44, C:0.52, G:0.00, T:0.05
Consensus pattern (7 bp):
CCAAACC
Found at i:25858833 original size:21 final size:20
Alignment explanation
Indices: 25858809--25858884 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 20
25858799 TGTAAACCTT
25858809 AAACCTCAAAAACCAAACCCC
1 AAACC-CAAAAACCAAACCCC
* *
25858830 AAACCCTAAACACTAAACCCC
1 AAACCC-AAAAACCAAACCCC
* *
25858851 AAACCCCAAACCCTAAACCCC
1 AAACCCAAAAACC-AAACCCC
*
25858872 AAACCCCAAAACC
1 AAACCCAAAAACC
25858885 CCGAACAGTA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 4 0.09
21 42 0.91
ACGTcount: A:0.49, C:0.46, G:0.00, T:0.05
Consensus pattern (20 bp):
AAACCCAAAAACCAAACCCC
Found at i:25858875 original size:28 final size:28
Alignment explanation
Indices: 25858802--25858886 Score: 107
Period size: 28 Copynumber: 3.0 Consensus size: 28
25858792 TATAATTTGT
* * **
25858802 AAACCTTAAACCTCAAAAACCAAACCCC
1 AAACCCTAAACCCCAAACCCCAAACCCC
* *
25858830 AAACCCTAAACACTAAACCCCAAACCCC
1 AAACCCTAAACCCCAAACCCCAAACCCC
25858858 AAACCCTAAACCCCAAACCCCAAAACCCC
1 AAACCCTAAACCCCAAACCCC-AAACCCC
25858887 GAACAGTAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 41 0.85
29 7 0.15
ACGTcount: A:0.47, C:0.46, G:0.00, T:0.07
Consensus pattern (28 bp):
AAACCCTAAACCCCAAACCCCAAACCCC
Done.